HunterZeo Storyline:
At the end of the most recent episode of the Mega Man X series, X fought defeated Sigma, who claimed that there was somebody who hated X even more and built Sigma's new and final body. Before he died, his explosion severely damaged Zero. Then, with his last bit of energy, Sigma fired a blast that severely damaged X and Zero, who destroyed the last vestige of Sigma. X was severely damaged, but a mysterious figure repaired him. He continued to live out his life relatively peacefully, preparing his plans for Elysium and using Zero's saber and memory to maintain peace. What nobody realized was that Zero's body was repaired, and overhauled into a more evolved form.

20 years later... X's dream of Elysium, a paradise for Humans and Reploids has become a reality. It is a massive floating citadel geosynchronously floating above western North America. It is fully self-contained and has a harmonious balance of humans and reploids, and the Maverick Virus is but a small memory. As a result, the few remaining Maverick Hunters have been relieved of duty, especially since X has Zero's Z-Saber and is powerful enough to take care of any problems with the few leftover Mavericks. All is peaceful in Elysium.
Then one day, X mysteriously disappears. Nobody knows where he went, but shortly afterwards, news breaks out of a Maverick uprising on the North American continent. Elysium is safe for now, but without X, fear quickly grows that the citadel will be attacked by the Mavericks. nobody knows the true nature or motive of these Mavericks, but they do know that these evil reploids are much stronger than any of the previous Mavericks, possibly more powerful than even Sigma himself! As a result, all the previous Hunters have been reenlisted, Repliforce has been reinstated with new officers, and new Hunters are being recruited and refitted for battle around the clock in an effort to help quell the NeoMaverick outbreak. Many NeoMavericks have been defeated, but just as many, if not more, of the new Hunters have been destroyed as well. The continent has been reduced to a war-torn battlefield, covered in carnage and waste. Elysium has had massively powerful forcefields enables, and it remains a safe haven for Reploids, and humans especially, but who knows how long it will stay that way? Something must be done. Either X must be found, or...

We shift our focus now toward the former state of Kansas, where a long, hard battle has left many Hunters and somewhat fewer NeoMavericks little more than pile of of scrap metal. A lone, grey Reploid with large wings stands on a robotic corpse, overlooking the mess. He scans the area and mutters to himself. Turning to leave, he spots movement, a single hand clawing its wat out of the rubble. Raising his arm cannon in preparation, the grey reploid moves toward the sole survivor of the battle. He grabs the hand and pulls up an armored, female Hunter, judging by her insignia.
"Are you ok?" he asks.
"You...are...Zero, aren't...you?" she struggles to reply.
"I was Zero, now I am the Fallen Angel. I will help you. Just relax." She passes out just before he teleports her away from the wreckage. Just before she loses consiousness, she hears him say something about the prophet.

"Ah, you're awake. I was afraid the transfer didn't work."
She opened her eyes to see the gray Reploid. "Huh? Where am I?"
"You're in my base of operations. Take a look at yourself," he responded, turning a mirror so she could look and see her new body. "What happened?!" She yelled, wide-eyed in alarm at seeing her reflection. "I thought we won the battle?"
"Well, you did. However, while you all cheered you victory, you were surprise-attacked by a small contingent of NeoMavericks. They hit your group with a Solar Flare. It wiped out everyone but you, and you were holding on by a thread. If I hadn't been folowing them, I wouldn't have found you, and you wouldn't have made it. It took 6 sub-tanks just to keep you alive long enough to transfer your consciousness into this new body. What do you think?"
She took another, longer look in the mirror. Her new body was mostly blue, with yellow and grey trim. It was slightly bulkier, than her previous armor, but it was a much stronger armor. Mentally, she checked her ablities. "I see you gave me some more abilities?"
"Yeah, I looked through your data file and checked out what you could do. I added a sonic blast attack, figuring you could use another offensive tactic. Also, I enhanced your energy whip's power level as best I could, but I'm still limited on resources. So you're name is Naia, right?"
"Yeah, yeah it is. And you're...?"
My official title is Zero the Fallen Angel, but I go by Angel, it's much shorter."

"So are those NeoMavericks that wasted my unit?"
"Yeah, they booked after a short fight. I've got their energy signals in my computr system, so we can track them down. But you need some training first, so they won't waste you."
"Alright, when can we start?"
"I knew when I found you still alive that you would be a good choice."
"For what?"
"I'm forming an elite Hunting Unit called HunterZeo. Congratulations, you just made my right hand Hunter. Of course, we'll need to recruit and upgrade more hunters, but you and I will make a good start."
"Cool, sounds like a romp."
"You're joking, right?"
Naia just laughed. "Let's get started."